Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 5:d9cbf833624e draft
planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Tue, 27 Oct 2020 12:46:55 +0000 |
| parents | 386438cd4c3b |
| children | 11a2a34f8a2b |
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| 4:386438cd4c3b | 5:d9cbf833624e |
|---|---|
| 157 reads_dict[chrom_stop_pos][tag], len(pileupread.alignment.query_sequence)) | 157 reads_dict[chrom_stop_pos][tag], len(pileupread.alignment.query_sequence)) |
| 158 if nuc == alt: | 158 if nuc == alt: |
| 159 count_alt += 1 | 159 count_alt += 1 |
| 160 if tag not in mut_read_dict: | 160 if tag not in mut_read_dict: |
| 161 mut_read_dict[tag] = {} | 161 mut_read_dict[tag] = {} |
| 162 mut_read_dict[tag][chrom_stop_pos] = alt | 162 mut_read_dict[tag][chrom_stop_pos] = (alt, ref) |
| 163 else: | 163 else: |
| 164 mut_read_dict[tag][chrom_stop_pos] = alt | 164 mut_read_dict[tag][chrom_stop_pos] = (alt, ref) |
| 165 elif nuc == ref: | 165 elif nuc == ref: |
| 166 count_ref += 1 | 166 count_ref += 1 |
| 167 elif nuc == "N": | 167 elif nuc == "N": |
| 168 count_n += 1 | 168 count_n += 1 |
| 169 elif nuc == "lowQ": | 169 elif nuc == "lowQ": |